Add filtering of invalid intensity values in log transformation, add message to warn user

[henninggaertner]

Description

fixes #41
log(0) is infinite, which is not the desired outcome for such a value. Therefore, they need to be filtered and dropped from the data, while notifying the users about the dropped values and urging them to change their pre-processing pipeline.

Changes

Add filtering, dropping and message in transformation.py
Adjust and add tests in test_transformation.py

Testing

Create a run with both protein and peptide import. Then manually change some intensity values to be 0 or negative in the run's dataframe folder. Then do the log transformation with the "dirty" data.
You should see a message about the dropped data.

PR checklist

Development

• If necessary, I have updated the documentation (README, docstrings, etc.)
• If necessary, I have created / updated tests.

Mergeability

• main-branch has been merged into local branch to resolve conflicts
• The tests and linter have passed AFTER local merge
• The code has been formatted with black

Code review

• I have self-reviewed my code.
• At least one other developer reviewed and approved the changes

[github-actions]

Coverage report

Click to see where and how coverage changed

File	Statements	Missing	Coverage	Coverage (new stmts)	Lines missing
protzilla
run.py
run_helper.py
runner.py
protzilla/data_analysis
differential_expression_helper.py					125, 143
differential_expression_kruskal_wallis.py					227
differential_expression_linear_model.py
differential_expression_mann_whitney.py					266
differential_expression_t_test.py
plots.py
protein_graphs.py
ptm_analysis.py					56, 123-125
protzilla/data_integration
di_plots.py
protzilla/data_preprocessing
outlier_detection.py
plots.py
protzilla/importing
ms_data_import.py					122, 276
protzilla/methods
data_analysis.py					21, 174, 250, 283, 308, 351, 916, 935
data_preprocessing.py
importing.py					144
protzilla/utilities
transform_dfs.py
utilities.py
ui/main
settings.py
ui/runs
fields.py
views.py					21, 250, 284
views_helper.py
ui/runs/forms
data_analysis.py					318-322, 379, 409, 445, 468, 1183, 1221, 1243
Project Total

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